Patents by Inventor Brian Chaikind

Brian Chaikind has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Publication number: 20250084392
    Abstract: This invention relates to compositions of matter, methods and instruments for directly recruiting repair templates to CRISPR nucleases to stimulate homology-directed repair. Molecular “tethers” are described which result in an increase in the local concentration of repair templates at the site of the double-strand break made by a nuclease, thereby enhancing the rate of homology directed repair and suppressing undesired edits.
    Type: Application
    Filed: January 4, 2023
    Publication date: March 13, 2025
    Inventors: Brian Chaikind, Christopher Lim
  • Publication number: 20250034595
    Abstract: The present disclosure provides compositions of matter, methods and instruments for nucleic acid-guided nickase/reverse transcriptase fusion enzyme editing of nucleic acids in live mammalian cells, and for tracking of editing events.
    Type: Application
    Filed: December 1, 2022
    Publication date: January 30, 2025
    Inventors: Brian Chaikind, Alex Hutagalung, Janine Mok
  • Publication number: 20240209329
    Abstract: Some aspects of this disclosure provide a fusion protein comprising a guide nucleotide sequence-programmable DNA binding protein domain (e.g., a nuclease-inactive variant of Cas9 such as dCas9), an optional linker, and a recombinase catalytic domain (e.g., a tyrosine recombinase catalytic domain or a serine recombinase catalytic domain such as a Gin recombinase catalytic domain). This fusion protein can recombine DNA sites containing a minimal recombinase core site flanked by guide RNA-specified sequences. The instant disclosure represents a step toward programmable, scarless genome editing in unmodified cells that is independent of endogenous cellular machinery or cell state.
    Type: Application
    Filed: May 26, 2023
    Publication date: June 27, 2024
    Applicant: President and Fellows of Harvard College
    Inventors: David R. Liu, Brian Chaikind, Jeffrey L. Bessen
  • Publication number: 20240043852
    Abstract: The present disclosure provides compositions of matter, methods and instruments for nucleic acid-guided nickase/reverse transcriptase fusion enzyme editing of nucleic acids in live mammalian cells.
    Type: Application
    Filed: October 20, 2023
    Publication date: February 8, 2024
    Applicant: Inscripta, Inc.
    Inventors: Brian Chaikind, Aamir Mir
  • Patent number: 11884924
    Abstract: The present disclosure provides compositions of matter, methods and instruments for nucleic acid-guided nickase/reverse transcriptase fusion enzyme editing of nucleic acids in live mammalian cells.
    Type: Grant
    Filed: February 14, 2022
    Date of Patent: January 30, 2024
    Assignee: Inscripta, Inc.
    Inventors: Brian Chaikind, Aamir Mir
  • Patent number: 11661590
    Abstract: Some aspects of this disclosure provide a fusion protein comprising a guide nucleotide sequence-programmable DNA binding protein domain (e.g., a nuclease-inactive variant of Cas9 such as dCas9), an optional linker, and a recombinase catalytic domain (e.g., a tyrosine recombinase catalytic domain or a serine recombinase catalytic domain such as a Gin recombinase catalytic domain). This fusion protein can recombine DNA sites containing a minimal recombinase core site flanked by guide RNA-specified sequences. The instant disclosure represents a step toward programmable, scarless genome editing in unmodified cells that is independent of endogenous cellular machinery or cell state.
    Type: Grant
    Filed: August 9, 2017
    Date of Patent: May 30, 2023
    Assignee: President and Fellows of Harvard College
    Inventors: David R. Liu, Brian Chaikind, Jeffrey L. Bessen
  • Publication number: 20220298502
    Abstract: The present disclosure provides compositions and methods to increase the percentage of edited cells in a cell population when employing nucleic-acid guided editing, as well as automated instruments for performing these methods.
    Type: Application
    Filed: March 16, 2022
    Publication date: September 22, 2022
    Inventor: Brian Chaikind
  • Publication number: 20220275377
    Abstract: The present disclosure provides compositions of matter, methods and instruments for nucleic acid-guided nickase/reverse transcriptase fusion enzyme editing of nucleic acids in live mammalian cells.
    Type: Application
    Filed: February 14, 2022
    Publication date: September 1, 2022
    Inventors: Brian Chaikind, Aamir Mir
  • Publication number: 20220145288
    Abstract: A HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols is provided. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. Methods for isolating clonal populations derived from individual fungal spores are also provided.
    Type: Application
    Filed: January 26, 2022
    Publication date: May 12, 2022
    Inventors: Vytas SunSpiral, Jennifer Fredlund, Hassan Abdulla, Paolo Boccazzi, Sean Poust, Sara da Luz Areosa Cleto, Brian Chaikind, Dylan Vaughan, Kenneth S. Bruno, Patrick Westfall, Edyta Szewczyk, Kyle Rothschild-Mancinelli, Arthur Muir Fong, III
  • Patent number: 11242524
    Abstract: A HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols is provided. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. Methods for isolating clonal populations derived from individual fungal spores are also provided.
    Type: Grant
    Filed: March 19, 2021
    Date of Patent: February 8, 2022
    Assignee: Zymergen Inc.
    Inventors: Vytas SunSpiral, Jennifer Fredlund, Hassan Abdulla, Paolo Boccazzi, Sean Poust, Sara da Luz Areosa Cleto, Brian Chaikind, Dylan Vaughan, Kenneth S. Bruno, Patrick Westfall, Edyta Szewczyk, Kyle Rothschild-Mancinelli, Arthur Muir Fong, III
  • Publication number: 20210371856
    Abstract: Methods, compositions, and kits for high throughput DNA assembly reactions in vitro. Modular CRISPR DNA constructs comprising modular insert DNA parts flanked by cloning tag segments comprising pre-validated CRISPR protospacer/protospacer adjacent motif sequence combinations.
    Type: Application
    Filed: August 3, 2021
    Publication date: December 2, 2021
    Inventors: Brian CHAIKIND, Hendrik Marinus VAN ROSSUM
  • Patent number: 11180753
    Abstract: HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. Methods can be carried out within optofluidic devices.
    Type: Grant
    Filed: December 20, 2019
    Date of Patent: November 23, 2021
    Assignee: Zymergen Inc.
    Inventors: Vytas SunSpiral, Jennifer Fredlund, Hassan Abdulla, Paolo Boccazzi, Sean Poust, Sara da Luz Areosa Cleto, Brian Chaikind, Dylan Vaughan, Kenneth S. Bruno, Patrick Westfall, Edyta Szewczyk, Kyle Rothschild-Mancinelli, Arthur Muir Fong, III
  • Patent number: 11130955
    Abstract: Methods, compositions, and kits for high throughput DNA assembly reactions in vitro. Modular CRISPR DNA constructs comprising modular insert DNA parts flanked by cloning tag segments comprising pre-validated CRISPR protospacer/protospacer adjacent motif sequence combinations. High throughput methods of CRISPRi and CRISPRa.
    Type: Grant
    Filed: August 15, 2019
    Date of Patent: September 28, 2021
    Assignee: Zymergen Inc.
    Inventors: Brian Chaikind, Hendrik M. Van Rossum, Aaron Miller, Paul Perkovich, Shawn Szyjka, Kedar Patel
  • Publication number: 20210284993
    Abstract: A HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols is provided. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. Methods for isolating clonal populations derived from individual fungal spores are also provided.
    Type: Application
    Filed: March 19, 2021
    Publication date: September 16, 2021
    Inventors: Vytas SunSpiral, Jennifer Fredlund, Hassan Abdulla, Paolo Boccazzi, Sean Poust, Sara da Luz Areosa Cleto, Brian Chaikind, Dylan Vaughan, Kenneth S. Bruno, Patrick Westfall, Edyta Szewczyk, Kyle Rothschild-Mancinelli, Arthur Muir Fong, III
  • Patent number: 11098305
    Abstract: Methods, compositions, and kits for high throughput DNA assembly reactions in vitro. Modular CRISPR DNA constructs comprising modular insert DNA parts flanked by cloning tag segments comprising pre-validated CRISPR protospacer/protospacer adjacent motif sequence combinations.
    Type: Grant
    Filed: August 8, 2019
    Date of Patent: August 24, 2021
    Assignee: Zymergen Inc.
    Inventors: Brian Chaikind, Hendrik Marinus van Rossum
  • Patent number: 10954511
    Abstract: A HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols is provided. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. Methods for isolating clonal populations derived from individual fungal spores are also provided.
    Type: Grant
    Filed: October 11, 2019
    Date of Patent: March 23, 2021
    Assignee: Zymergen Inc.
    Inventors: Vytas SunSpiral, Jennifer Fredlund, Hassan Abdulla, Paolo Boccazzi, Sean Poust, Sara da Luz Areosa Cleto, Brian Chaikind, Dylan Vaughan, Kenneth S. Bruno, Patrick Westfall, Edyta Szewczyk, Kyle Rothschild-Mancinelli, Arthur Muir Fong, III
  • Publication number: 20200123540
    Abstract: The disclosure describes methods, compositions, and kits for high throughput DNA assembly reactions in vitro. The disclosure further describes modular CRISPR DNA constructs comprising modular insert DNA parts flanked by cloning tag segments comprising pre-validated CRISPR protospacer/protospacer adjacent motif sequence combinations.
    Type: Application
    Filed: August 8, 2019
    Publication date: April 23, 2020
    Inventors: Brian Chaikind, Hendrik Marinus van Rossum
  • Publication number: 20200123535
    Abstract: The present disclosure provides a HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition.
    Type: Application
    Filed: December 20, 2019
    Publication date: April 23, 2020
    Inventors: Vytas SunSpiral, Jennifer Fredlund, Hassan Abdulla, Paolo Boccazzi, Sean Poust, Sara da Luz Areosa Cleto, Brian Chaikind, Dylan Vaughan, Kenneth S. Bruno, Patrick Westfall, Edyta Szewczyk, Kyle Rothschild-Mancinelli, Arthur Muir Fong, III
  • Publication number: 20200071693
    Abstract: The present disclosure provides a HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition.
    Type: Application
    Filed: October 11, 2019
    Publication date: March 5, 2020
    Inventors: Vytas Sunspiral, Jennifer Fredlund, Hassan Abdulla, Paolo Boccazzi, Sean Poust, Sara da Luz Areaosa Cleto, Brian Chaikind, Dylan Vaughan, Kenneth S. Bruno, Patrick Westfall, Edyta Szewczyk, Kyle Rothschild-Mancinelli, Arthur Muir FONG, III
  • Publication number: 20200056191
    Abstract: The disclosure describes methods, compositions, and kits for high throughput DNA assembly reactions in vitro. The disclosure further describes modular CRISPR DNA constructs comprising modular insert DNA parts flanked by cloning tag segments comprising pre-validated CRISPR protospacer/protospacer adjacent motif sequence combinations. High throughput methods of CRISPRi and CRISPRa are also disclosed.
    Type: Application
    Filed: August 15, 2019
    Publication date: February 20, 2020
    Inventors: Brian Chaikind, Hendrik M. Van Rossum, Aaron Miller, Paul Perkovich, Shawn Szyjka, Kedar Patel